LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls

variable        b index 0

variable	x index 50
variable	y index 20
variable	d index 20
variable	v index 5
variable	w index 2

units		lj
dimension       2
atom_style	bond
boundary        f f p

lattice		hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region		box block 0 $x 0 $y -0.5 0.5
region		box block 0 50 0 $y -0.5 0.5
region		box block 0 50 0 20 -0.5 0.5
create_box	1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
  2 by 1 by 1 MPI processor grid
region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region		circle sphere 11 6.7735026918962581988 0.0 10
create_atoms	1 region circle
Created 361 atoms
  Time spent = 0.000778913 secs
mass		1 1.0

velocity	all create 0.5 87287 loop geom
velocity        all set $v $w 0 sum yes
velocity        all set 5 $w 0 sum yes
velocity        all set 5 2 0 sum yes

pair_style	lj/cut 2.5
pair_coeff	1 1 10.0 1.0 2.5

bond_style      harmonic
bond_coeff      1 10.0 1.2

# need to preserve 1-3, 1-4 pairwise interactions during hard collisions

special_bonds   lj/coul 0 1 1
  0 = max # of 1-2 neighbors
  1 = max # of special neighbors
create_bonds    many all all 1 1.0 1.5
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 42 29 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d/newton
      bin: standard
Added 1014 bonds, new total = 1014
  6 = max # of 1-2 neighbors
  6 = max # of special neighbors

neighbor	0.3 bin
neigh_modify	delay 0 every 1 check yes

fix		1 all nve

fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5

comm_style      tiled
comm_modify     cutoff 10.0   # because bonds stretch a long ways
fix             10 all balance 50 0.9 rcb

#compute         1 all property/atom proc
#variable        p atom (c_1%10)+1
#dump            2 all custom 50 tmp.dump id v_p x y z

#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}

thermo_style    custom step temp epair press f_10[3] f_10
thermo          100

run		10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 10
  binsize = 1.4, bins = 42 29 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.156 | 5.167 | 5.177 Mbytes
Step Temp E_pair Press f_10[3] f_10 
       0    25.701528   -2.2032569    3.1039469            2    1.0193906 
     100    27.623422    -6.228166    2.6542136    1.0803324    1.0027701 
     200     33.35302   -15.746749    3.2018248    1.1246537    1.0027701 
     300     39.17734     -24.1557    4.9116986    1.1468144    1.0027701 
     400    41.660701   -27.615203    8.6214678    1.2077562    1.0027701 
     500    37.154935   -24.096954    3.2656298    1.2243767    1.0083102 
     600    35.062196   -21.527799    2.3688444    1.1800554    1.0027701 
     700    36.962955   -22.265373    3.0233424    1.1800554    1.0083102 
     800    38.514356   -24.625735    5.2876402    1.2077562    1.0027701 
     900    37.840168   -24.069158     4.443617    1.2022161    1.0083102 
    1000    36.429396   -23.978878    7.2603394    1.1966759    1.0027701 
    1100     34.75827   -22.743232    6.6304628    1.1745152    1.0083102 
    1200    31.057199    -21.46544    3.7869701    1.1634349    1.0083102 
    1300    33.127345   -22.426161     5.824726    1.0858726    1.0027701 
    1400    31.678654   -21.604473    3.2219261    1.0360111    1.0083102 
    1500    28.345212   -18.030807   0.93335223    1.1191136    1.0027701 
    1600    26.031412   -15.389052   0.82549542    1.1080332    1.0027701 
    1700    25.082832    -13.48625    1.0006592    1.0858726    1.0027701 
    1800    25.673875   -13.965883   0.54607043    1.0692521    1.0027701 
    1900    26.530842   -13.979318    2.0285449    1.1024931    1.0027701 
    2000    25.910771   -14.244515    1.9592232    1.1191136    1.0027701 
    2100    28.505636   -16.220559    1.7154775    1.1191136    1.0027701 
    2200    28.142753   -15.564302    2.9946076    1.1135734    1.0027701 
    2300    26.606225   -13.734442    1.4589278    1.0083102    1.0083102 
    2400    25.664988   -12.389759    1.3450183    1.0360111    1.0027701 
    2500    25.145328   -11.815173   0.48162788    1.0360111    1.0027701 
    2600    26.654868   -13.916929    2.8361012    1.0581717    1.0083102 
    2700      27.3758   -15.495452    4.1206412    1.0360111    1.0027701 
    2800     23.60864   -14.520038    1.8948923    1.0193906    1.0027701 
    2900    20.604557   -12.901121   0.17526991    1.0138504    1.0027701 
    3000    20.852473   -12.756946  -0.44987285    1.0360111    1.0027701 
    3100    21.934986   -12.797691   0.76186765    1.0415512    1.0027701 
    3200    23.293263   -12.368233  0.021937309    1.0526316    1.0027701 
    3300    22.091492    -10.88605  0.013006632    1.0415512    1.0083102 
    3400    23.535429   -10.937804    2.0738989    1.0360111    1.0027701 
    3500    24.503573   -12.202994     1.126785    1.0581717    1.0027701 
    3600     23.54503   -12.745709   0.39022194    1.0858726    1.0027701 
    3700    22.658187   -10.986188  -0.18869692    1.0692521    1.0027701 
    3800    21.282045   -9.7879088 -0.061253454    1.0193906    1.0027701 
    3900    20.571754   -9.1157993   -1.0178917    1.0526316    1.0027701 
    4000    23.779702   -10.230328    1.0778525    1.0581717    1.0083102 
    4100    23.675854    -10.63724   0.59402249    1.0415512    1.0027701 
    4200    24.058963    -11.89505    0.3866378    1.0526316    1.0027701 
    4300    22.683721   -11.358978    1.8269036    1.0470914    1.0083102 
    4400    23.002345   -11.081443    0.4529456    1.0415512    1.0027701 
    4500    21.984542   -10.233276  -0.60718244    1.0415512    1.0083102 
    4600    22.079237    -9.979061   0.53013572    1.0415512    1.0027701 
    4700    22.336961   -10.323583  -0.37512832    1.0249307    1.0027701 
    4800    23.351699   -10.143724   0.95694397    1.0470914    1.0027701 
    4900    23.643954   -10.687354    1.6062522    1.0858726    1.0083102 
    5000    25.158132   -11.532398    1.3083639    1.0914127    1.0027701 
    5100    23.755521   -10.978548   0.60587307    1.0470914    1.0027701 
    5200    21.842692   -10.443216  -0.41185899    1.0637119    1.0027701 
    5300    22.828066   -10.871114    1.1754353    1.0470914    1.0027701 
    5400    24.883977    -12.39165   0.65101173    1.0470914    1.0027701 
    5500    22.908286   -11.419431    1.4712698    1.0637119    1.0027701 
    5600    22.718634   -12.083974    1.5706808    1.0526316    1.0027701 
    5700    23.080763   -11.464882    1.2979578    1.0304709    1.0083102 
    5800    21.877026   -11.483185     0.279772    1.0360111    1.0027701 
    5900    22.526809   -10.868636   0.37121786    1.0637119    1.0083102 
    6000    22.908857   -10.311118   0.58244569    1.0526316    1.0083102 
    6100    22.399847   -10.222706   0.87875674    1.0858726    1.0027701 
    6200    22.623463   -10.035541  -0.25811274    1.0304709    1.0027701 
    6300    21.518006   -10.017552  -0.98187611    1.0470914    1.0083102 
    6400    21.269816   -11.297716   0.20058535    1.0138504    1.0027701 
    6500    23.362834   -11.263306   0.47670072    1.0692521    1.0027701 
    6600    23.705236   -12.358492  -0.63286237    1.0027701    1.0027701 
    6700    22.410623   -10.849516   0.57027834    1.0581717    1.0083102 
    6800    21.661639   -9.3981379   0.38726515    1.0470914    1.0027701 
    6900    21.856521   -8.8451751  0.053822789    1.0304709    1.0027701 
    7000    21.069495   -8.6443387  -0.10412144    1.0193906    1.0027701 
    7100    22.305494   -10.098469  -0.22662961    1.0581717    1.0027701 
    7200     23.52884   -11.055929 -0.099869868    1.0692521    1.0027701 
    7300    24.042008   -11.411758    2.0528788    1.0415512    1.0027701 
    7400    22.870777   -12.408763   0.33346225    1.0249307    1.0027701 
    7500    21.290152   -10.963058   0.26940112    1.0083102    1.0027701 
    7600    21.702686    -10.36214   0.84057004    1.0083102    1.0027701 
    7700    22.478034   -10.832724  -0.70855164    1.0747922    1.0027701 
    7800    22.856853   -11.161008  -0.88354803    1.0083102    1.0083102 
    7900    22.579842   -10.789899   0.40865274    1.0360111    1.0027701 
    8000    24.364281   -12.116023  -0.44788445    1.0249307    1.0083102 
    8100    22.993409   -10.261331   0.44712215    1.0193906    1.0027701 
    8200    23.006207   -10.723372    1.2357091    1.0415512    1.0083102 
    8300    23.292233   -10.041314     2.143692    1.0581717    1.0027701 
    8400    21.658087   -10.089378  -0.25838681    1.0083102    1.0027701 
    8500    23.268456   -10.356603  0.089787317    1.0526316    1.0083102 
    8600    22.572019    -10.32801   0.12320758    1.0526316    1.0027701 
    8700    22.970465   -10.662456   0.57027398    1.0581717    1.0083102 
    8800    23.515552   -10.415842    1.0048598    1.0138504    1.0083102 
    8900    22.733961   -10.343495   0.19917627    1.0360111    1.0083102 
    9000    21.835458   -9.8740971   -1.0653164    1.0193906    1.0027701 
    9100    22.062821   -9.2303832   0.21428267    1.0415512    1.0083102 
    9200    23.020404   -10.321542  -0.48757848    1.0193906    1.0083102 
    9300    22.529362   -9.2916938   0.57056277    1.0415512    1.0027701 
    9400    23.301911   -10.538876   0.80637627    1.0138504    1.0027701 
    9500    21.984286   -9.4754676  -0.19048233    1.0193906    1.0027701 
    9600    23.710224   -10.274983   0.72268146    1.0249307    1.0027701 
    9700    22.317038   -9.3509008  -0.45727658    1.0360111    1.0027701 
    9800     23.41615   -10.026331  -0.45909049    1.0415512    1.0027701 
    9900    22.130299    -11.18528  -0.15359132    1.0747922    1.0027701 
   10000    23.273859   -11.337403    0.4036321    1.0304709    1.0083102 
Loop time of 1.18289 on 2 procs for 10000 steps with 361 atoms

Performance: 3652073.393 tau/day, 8453.874 timesteps/s
97.0% CPU use with 2 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.25191    | 0.25685    | 0.2618     |   1.0 | 21.71
Bond    | 0.097655   | 0.098332   | 0.099009   |   0.2 |  8.31
Neigh   | 0.53258    | 0.53993    | 0.54728    |   1.0 | 45.65
Comm    | 0.13457    | 0.15372    | 0.17288    |   4.9 | 13.00
Output  | 0.0013587  | 0.0016007  | 0.0018427  |   0.6 |  0.14
Modify  | 0.074109   | 0.074314   | 0.074518   |   0.1 |  6.28
Other   |            | 0.05813    |            |       |  4.91

Nlocal:    180.5 ave 182 max 179 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost:    172.5 ave 175 max 170 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs:    1421 ave 1488 max 1354 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 2842
Ave neighs/atom = 7.87258
Ave special neighs/atom = 5.61773
Neighbor list builds = 4884
Dangerous builds = 0
Total wall time: 0:00:01
